Naruto: The Hidden Prodigy
by Nakata Kuzuki
Summary: Naruto Uzumaki-Namikaze, born on October 10 along with his siblings Mito and Menma. Growing up Naruto tries to distant himself from his family which leads Naruto to train by himself which leads to Naruto being secretly recruited into Root Anbu. Naruto becomes a hidden prodigy from then on. Sharingan/Mokuton Naruto. Naruto x Toka x Satsuki? Sasuke x Karin


**Hey everyone, this is the rewritten first chapter. Not much changed in this chapter as I just added a few more paragraphs to describe some of the events of the Kyuubi attack. I also changed Takashi's name to Menma because I like the name Menma better and while I was writing this story previously I kept forgetting his name. With the whole Root organization with Danzo deal is that I might make them good and I won't be killing them off like I did before as I believe that was just progressing the story too fast.**

 **On another side note I will be starting a pole to see if I should give Naruto the Rinnegan or not, because I can write this story with and without it.**

 **The Hidden Prodigy (Rewritten 12-22-15)**

 **Summary: Naruto Uzumaki-Namikaze, born on October 10 along with his younger sister Mito and younger brother Menma. Narutos siblings are the ones who become the jinchuriki of the Kyuubi's chakra while he gets the soul. Growing up Naruto tries to distant himself from his family which leads Naruto to train by himself which leads to Naruto being secretly recruited into Root Anbu. Naruto becomes a hidden prodigy from then on with the desire to protect his family which awakens his bloodline the Sharingan. Naruto also unlocks the Senju bloodline the Mokuton. Naruto becomes friends with Sasuke early on. Sharingan/Mokuton Naruto. Naruto x Toka x Satsuki (Sasuke's twin sister) Sasuke x Karin**

Chapter 1 Prologue: The Beginning of a Legend

There was the sound of the Kyuubi roaring in anger underneath the boss toad Gambunta while in front of the kyuubi stood five adults along with three babies. The adults being Hiruzen Sarutobi, Minato Namikaze, Tsunade Senju, Kushina Uzumaki, and Jiraiya. The three babies being Naruto, Mito, and Menma Uzumaki-Namikaze. The adults were all in a five points around the Kyuubi going through hand seals to seal the Kyuubi's chakra into the two younger babies and the kyuubi's soul into Naruto. Minato then added an eight trigram seal onto each baby to finish the sealing.

This devistating disaster happened only mere hours ago by one man. This masked man who claimed to be Uchiha Madara killed the Sandaime's wife along with the nurse who was helping at the time. The masked man was holding Menma becasue Mito and Naruto were already at the Safe house and asked for Minato to step away from the jinchuriki or the baby will die in its first minute of living. The masked man managed to seperate Minato from Kushina as he warped both himself and Kushina away from the Battle field. He used his Sharingan eye to control the Kuubi within the seal on Kushina's stomach that was weakened from the pregnancy and was easily able to get the Kyuubi out of the seal bringing it out into the living world once again in a long time. Before the Kyuubi was able to crush a weakened Kushina, Minato was able to Hirashin to her and Hirashin away with her before she could get crushed. The Masked man the Summoned the Kyuubi into the village while Minato brought Kushina to safety at the Safe House with the three babies. It was then that Minato went out to fight the masked man break the control contract he had on the Kyuubi but everytime he went for an attack the masked man just slipped through him to avoid it. After the fight ended with the masked man retreating after taking a Rasengan to the back, Minato Hirashined to the Hokage Monument to Hirashin a Tailed Beast Ball away from the village and followed up with using Hirashin to flash the Kyuubi away from the village.

While Minato was dealing with the Kyuubi Tsunade Senju was rushing on the battlefield healing up injured Shinobi. She was supposed to help Kushina give Birth to the trio of babies but she didn't arive on time due to Kushina going into Labor earlier than they expected. Once she saw that Minato used Hirashin on the Kyuubi to get it away from the village she started running off in the direction the Kyuubi was now. She was soon running along with her Sensei Sarutobi Hiruzen and her knucklehead of a team mate Jiraiya as they went off towards the on going fight between Gambunta and the Kyuubi.

Minato after leaving Gambunta on the Kyuubi Hirashined to the Safe House to bring Kushina and the trio of babies with him. Kushina, after taking a soldier pill wrapped the Kyuubi in her chakra chains waiting for Minato to finished whatever he was doing. It was then that Tsunade, Jiraiya, and Hiruzen arrived and after talking for a momnent they seperated into a five point star which included her. Minato quickly came over and made a altar and placed the three babies on top of it while telling Kushina the plan that he wanted to use on the Kyuubi.

This was at the point where they were now.

"Fuin" Minato yelled as the seals on each baby glowed before disappearing.

All you could hear on the battlefield now was the fires burning and the moaning of the injured shinobi that got injured fighting the Kyuubi.

"Minato, we need to get Kushina and your children to the hospital do you think you still have enough chakra to flash us there?" Tsunade asked going into medic mode.

"Yes I believe I do have enough" walking over to his wife, children, and Tsunade he grabbed a hold of them flash them to the lobby of the hospital where there was wounded being wheeled around everywhere.

* * *

The Next Morning: Council Room

Minato walked into the room and sat in the chair meant for the Hokage and began the meeting.

"Everyone I would like to start the meeting off with the incident that happened last night. As we all know last night the Kyuubi appeared and attacked the village which destroyed a quarter of the village and killed a third of our shinobi. I would like to say the way I along with Hiruzen Sarutobi, Tsunade Senju, Kushina Uzumaki, and Jiraiya defeated the Kyuubi by sealing its chakra into my newborn children Mito and Menma Uzumaki-Namikaze while we sealed its soul into my newborn child Naruto Uzumaki-Namikaze. I did it that way because I believe the chakra will be easier to control without the soul present." Minato finished while looking around the room for any questions.

A random civilian council member speaks up after a moment "Hokage-sama will we ever be in danger of the children while their in the village? And if you are saying that these are your children does that mean you married Kushina Uzumaki?"

"Yes I plan on telling the entire village in a month about my marriage and no you will not be endanger of my children in the village. I would like to have the village see my children as heroes for keeping the Kyuubi locked up. I am also going to place a law stating that the younger generation does not know about my children being the jinchuriki" answered Minato with a serious expression on showing he wasn't kidding.

One of the elders named Danzo Shimura spoke up next "I believe we should turn these jinchuriki into weapons. My Root program would be the best option to train them"

Minato never liked Danzo he was always too manipulative and power hunger. Minato the yelled out at Danzo " You will not be turning my children into mindless drones of yours Danzo. As the matter of fact I hereby disband Root. Root is most needed during war times and we are no longer at war so there is no need to have Root active."

Danzo gritted his teeth in anger not liking how things gone for him as he got up from his seat and walked out the door having no need to stay at the meeting.

"Ok now onto other business" Minato said as the council continued the meeting.

* * *

Three years later: Uzumaki-Namikaze compound

In the compound there was a commotion going on, or to be more precise, there was two three year olds running around being chased by their mother.

"Get back here Mito, Menma you need to get dressed" Kushina called out starting to get irritated with her children.

Right when the two children were about to run out the back door into the front yard Tsunade scooped up the two energetic children. "You two need to listen to your mother. Now go get dressed" all she got from the kids were "ok Baa-chan" then they ran to there rooms.

Where is Naru-chan I haven't seen him yet this morning?" Tsunade asked as she walked over to the dining room table and sat down on a chair.

"He is in his room trying to read a book. Should three year olds be this smart because I don't remember trying to read until I was four?" Kushina asked in a worried tone hoping to get an answer from the best medic ninja in the world.

"Well yes three year olds shouldn't be trying to read yet and they should be ready to understand much of anything until their four years old but they are the children of two kage level shinobi. My children are the same so I don't see a problem with them being smart when they are older" she answered thinking about her two three year old children.

It happened a while ago when Jiraiya came to her asking her to return to the village and become the head of the hospital here. Jiraiya helped her come out of her depression by confessing to her and saying that he would always be their for her with her liking it or not. It was a couple years later when Tsunade became pregnant with twins one a boy the other a girl. With Tsunade being the worlds greatest medic she easily made her body be able to have children since she did have to continue the Senju line.

After the Kyuubi attack Minato announced to the village about the law stating no talking about his children being the jinchuriki of the Kyuubi. The civilians were worried about the children but after a quick lecture from Minato the villagers started welcoming the three children. While some villagers and shinobi simply ignore the children most greet them in a friendly matter.

There was also delegation from Kumagakure wanting to have a peace treaty and trading routes to be discussed. The Raikage also came along to show their seriousness in wanting the treaty to be finalized. What came next was one of the shinobi in the entourage with the Raikage tried to kidnap the heiress of the Hyuga clan, Hinata Hyuga was lucky enough to be saved by another Kumo shinobi that was sent from the Raikage to watch him. The Raikage apologized for his shinobi's act and that he will be properly interrogated back in Kumo and that now he has a reason to interrogate his council to get rid of some coruptted councilers.

The first chunin exams since the treaty has come and gone and Konoha got to see some of the genin teams from Kumo and they got some shinobi into the finals, but didn't win the exam.

* * *

One year later: With Naruto at his Secret Training ground behind the Hokage Monument

Naruto was sitting alone on a tree branch at his training ground he created behind the Hokage Monument since his parents weren't going to teach him yet because he was still too young. Naruto was reading a book on chakra control until he finally got the idea down on how to balance a leaf on his finger tips.

"Man this is going to take a while to get down. After I get this down I can work on the tree walking exercise since I know I would have large chakra reserves thanks to being an Uzumaki. In the book I read it said that as long as I have something I wish to protect then my growth as a shinobi is limitless" he thought out loud.

Hiding in another tree stood Danzo watching the young Namikaze to see if the young blonde has the same potential his siblings have with the Kyuubi's chakra. 'He has some real potential if trained right as a shinobi though he doesn't have the same amount of potential as his siblings but potential is still there'. He started walk over to Naruto until he stood a yard behind him. Naruto who still hasn't noticed Danzo behind him started to balance a leaf on his fingers.

"Young Namikaze it seems like you are ready to become a real shinobi, but why at such a young age" Danzo asked testing the boy to see why he wants to become a shinobi.

Naruto jumped in surprise of the voice not expecting anybody else to be there with him. Naruto looked up at the elder bowing his head he replied "Hello Danzo-sama to answer your question I am beginning my training early because I would like to get stronger to protect my village and family even if they don't know I am training this early in my life. A true shinobi is one that lives and protects from the shadows while they use deception to fool others. Shinobi also do the jobs that others aren't willing to do. So if I have to keep my skills and intelligence a secret from everyone to protect my village and family then so be it.

Danzo was surprised on how smart and respectful the boy was. Children his age shouldn't be this smart or knowledgeable in things like this. 'This boy has more potential than I first thought. He would be a perfect shinobi in my Root Anbu if he is willing to join and keep it a secret from everyone'. "Young Namikaze I can see a lot of potential in you as a shinobi. If you are willing to I can make you a deal on me training you from now on?"

On the inside Naruto was eager to be trained by a shinobi of the caliber as Danzo but on the outside Naruto didn't show any emotion. "Danzo-sama if I may ask what is it that you get on your side of the deal?"

"On my side of the deal you will join my Root Anbu organization as one of my shinobi who does the missions that the village does not want anybody knowing that we do them. You will be trained in all arts of the shinobi to become a weapon for the village so you can protect the village and your family from the shadows like a true shinobi. So Young Namikaze how would you like to join Root Anbu and become a true shinobi?"

Naruto looked up at Danzo and got on one knee with his forest green eyes turning into bloody red with one tomoe in each eye. Bowing to Danzo he says "Then I am your shinobi to use Lord Danzo".

Danzo was very surprised to see the sharingan in Naruto since he wasn't an Uchiha. 'I guess I was wrong again this boy probably has more potential than his siblings. I guess I just gained an invaluable asset in Root'.

Danzo didn't know how right he is


End file.
